It seems your comment on Dale M's answer is basically in the ballpark: it's about administration of justice, or at least it used to be.
Criminal law and criminal procedure are the exclusive competence of the federal government (Constitution Act, 1867, s. 91(27)), hence by default, the Criminal Code applies in its entirety across the country. However, territories are federal entities and so in theory, any federal matter could be devolved to the territorial legislatures. This is hinted at with the s. 8 in your question. However, with the exception of some Aboriginal matters, the territorial acts are clear that the territorial legislatures do not have any competencies beyond that of the provinces (Yukon Act s. 20(1), Northwest Territories Act s. 25(1), Nunavut Act s. 23(2))
This makes our job easier: since the territorial legislatures can't legislate on criminal matters, any inconsistency with the Criminal Code would have to lie directly in those three territorial acts. While I could have missed something, I was unable to find any inconsistency in either the Yukon or Northwest Territory acts. So why does s. 8 of the Criminal Code exist? It seems to be a matter of how the legislation was historically structured: The Criminal Code would set the country-wide default, and any derogations could be placed in the territorial acts. See for example The King v. Standard Soap Company, 1907 CanLII 134 (NWT SC):
When the Criminal Code, 1892, was enacted, it was, by sec. 983, made applicable to the North-West Territories, except in so far as it was inconsistent with the provisions of the North-West Territories Act and the amendments thereto. As far as this case is concerned, the only Changes made in the Code by that Act are that instead of an indictment being presented by a grand jury to the Court where a person is charged with a criminal offence, the proceedings are commenced by a charge in writing setting forth the offence in the same manner as in an indictment.
Grand juries no longer exist in Canada, so this inconsistency doesn't either (I speculate the original reason would have been the difficulty and expense of convening grand juries in such a sparsely populated territory).
As for Nunavut, well it seems Parliament threw the historical structure out the Peace Tower window. If you search for "Yukon" or "Northwest" in the Criminal Code, you'll find about 20 results each where they are mostly being treated the same as the provinces. If you search for "Nunavut", you'll get about 140 results. Therefore, I will leave finding any potential inconsistencies as an exercise to the reader.